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GC GC vitamin D binding protein [ Homo sapiens (human) ]

Gene ID: 2638, updated on 22-Jan-2024

Summary

Official Symbol
GCprovided by HGNC
Official Full Name
GC vitamin D binding proteinprovided by HGNC
Primary source
HGNC:HGNC:4187
See related
Ensembl:ENSG00000145321 MIM:139200; AllianceGenome:HGNC:4187
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DBP; VDB; GRD3; VDBG; VDBP; GcMAF; DBP/GC; Gc-MAF; DBP-maf; HEL-S-51
Summary
The protein encoded by this gene belongs to the albumin gene family. It is a multifunctional protein found in plasma, ascitic fluid, cerebrospinal fluid and on the surface of many cell types. It binds to vitamin D and its plasma metabolites and transports them to target tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]
Expression
Restricted expression toward liver (RPKM 1264.0) See more
Orthologs
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Genomic context

Location:
4q13.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (71741693..71805520, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (75084117..75147957, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (72607410..72671237, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:72458772-72459481 Neighboring gene uncharacterized LOC107986285 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:72479894-72481093 Neighboring gene uncharacterized LOC105377271 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:72519382-72520581 Neighboring gene RNA, 5S ribosomal pseudogene 163 Neighboring gene VISTA enhancer hs2570 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:72836369-72836534 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:72897326-72897928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:72960191-72960690 Neighboring gene neuropeptide FF receptor 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:72977919-72979118 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:73019056-73019842 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 3 Neighboring gene Sharpr-MPRA regulatory region 5509

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Association between liver-specific gene polymorphisms and their expression levels with nonalcoholic fatty liver disease.
EBI GWAS Catalog
Common genetic determinants of vitamin D insufficiency: a genome-wide association study.
EBI GWAS Catalog
Genome-wide association analysis of circulating vitamin D levels in children with asthma.
EBI GWAS Catalog
Genome-wide association study of circulating vitamin D levels.
EBI GWAS Catalog
Genome-wide association study of circulating vitamin D-binding protein.
EBI GWAS Catalog
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
EBI GWAS Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables calcidiol binding IDA
Inferred from Direct Assay
more info
PubMed 
enables vitamin D binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables vitamin transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in transport IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in vitamin D metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in vitamin transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
involved_in vitamin transport TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
vitamin D-binding protein
Names
epididymis secretory protein Li 51
gc protein-derived macrophage activating factor
gc-globulin
group-specific component (vitamin D binding protein)
vitamin D-binding alpha-globulin
vitamin D-binding protein-macrophage activating factor
NP_000574.2
NP_001191235.1
NP_001191236.1
XP_006714240.1
XP_054205648.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012837.3 RefSeqGene

    Range
    26442..68824
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000583.4NP_000574.2  vitamin D-binding protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_000574.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is a predominant transcript. This variant and variant 2 encode the same isoform (1).
    Source sequence(s)
    AA702473, AK223458, X03178
    Consensus CDS
    CCDS3550.1
    UniProtKB/Swiss-Prot
    B4DPP2, D6RAK8, P02774, Q16309, Q16310, Q53F31, Q6GTG1
    UniProtKB/TrEMBL
    V9HWI6
    Related
    ENSP00000273951.8, ENST00000273951.13
    Conserved Domains (2) summary
    smart00103
    Location:19201
    ALBUMIN; serum albumin
    pfam09164
    Location:405469
    VitD-bind_III; Vitamin D binding protein, domain III
  2. NM_001204306.1NP_001191235.1  vitamin D-binding protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_001191235.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR and encodes the same isoform 1, as compared to variant 1.
    Source sequence(s)
    AA702473, AK223458
    Consensus CDS
    CCDS3550.1
    UniProtKB/Swiss-Prot
    B4DPP2, D6RAK8, P02774, Q16309, Q16310, Q53F31, Q6GTG1
    UniProtKB/TrEMBL
    V9HWI6
    Conserved Domains (2) summary
    smart00103
    Location:19201
    ALBUMIN; serum albumin
    pfam09164
    Location:405469
    VitD-bind_III; Vitamin D binding protein, domain III
  3. NM_001204307.1NP_001191236.1  vitamin D-binding protein isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate 5' sequence which contains an upstream in-frame AUG start codon, as compared to variant 1. The resulting isoform (2) has a longer N-terminus, as compared to isoform 1.
    Source sequence(s)
    AA702473, AC024722, AK223458, AK309595, AK315853
    Consensus CDS
    CCDS56332.1
    UniProtKB/TrEMBL
    V9HWI6
    Related
    ENSP00000421725.1, ENST00000504199.5
    Conserved Domains (2) summary
    smart00103
    Location:38220
    ALBUMIN; serum albumin
    pfam09164
    Location:424488
    VitD-bind_III; Vitamin D binding protein, domain III

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    71741693..71805520 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714177.3XP_006714240.1  vitamin D-binding protein isoform X1

    UniProtKB/TrEMBL
    V9HWI6
    Related
    ENSP00000422664.1, ENST00000509740.5
    Conserved Domains (1) summary
    smart00103
    Location:19201
    ALBUMIN; serum albumin

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    75084117..75147957 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349673.1XP_054205648.1  vitamin D-binding protein isoform X1

    UniProtKB/TrEMBL
    V9HWI6